LCOV - code coverage report
Current view: top level - src/motion - input_cp2k_vib.F (source / functions) Hit Total Coverage
Test: CP2K Regtests (git:b195825) Lines: 119 119 100.0 %
Date: 2024-04-20 06:29:22 Functions: 4 4 100.0 %

          Line data    Source code
       1             : !--------------------------------------------------------------------------------------------------!
       2             : !   CP2K: A general program to perform molecular dynamics simulations                              !
       3             : !   Copyright 2000-2024 CP2K developers group <https://cp2k.org>                                   !
       4             : !                                                                                                  !
       5             : !   SPDX-License-Identifier: GPL-2.0-or-later                                                      !
       6             : !--------------------------------------------------------------------------------------------------!
       7             : 
       8             : ! **************************************************************************************************
       9             : !> \brief builds the input structure for the VIBRATIONAL_ANALYSIS module
      10             : !> \par History
      11             : !>      01.2008 [tlaino] Teodoro Laino - University of Zurich
      12             : !>                       Creating an own module for vibrational analysis
      13             : !> \author [tlaino]
      14             : ! **************************************************************************************************
      15             : MODULE input_cp2k_vib
      16             :    USE cp_output_handling,              ONLY: add_last_numeric,&
      17             :                                               cp_print_key_section_create,&
      18             :                                               debug_print_level,&
      19             :                                               low_print_level,&
      20             :                                               medium_print_level,&
      21             :                                               silent_print_level
      22             :    USE cp_units,                        ONLY: cp_unit_to_cp2k
      23             :    USE input_constants,                 ONLY: do_rep_blocked,&
      24             :                                               do_rep_interleaved,&
      25             :                                               ms_guess_atomic,&
      26             :                                               ms_guess_bfgs,&
      27             :                                               ms_guess_molden,&
      28             :                                               ms_guess_restart,&
      29             :                                               ms_guess_restart_vec
      30             :    USE input_keyword_types,             ONLY: keyword_create,&
      31             :                                               keyword_release,&
      32             :                                               keyword_type
      33             :    USE input_section_types,             ONLY: section_add_keyword,&
      34             :                                               section_add_subsection,&
      35             :                                               section_create,&
      36             :                                               section_release,&
      37             :                                               section_type
      38             :    USE input_val_types,                 ONLY: integer_t,&
      39             :                                               real_t
      40             :    USE kinds,                           ONLY: dp
      41             :    USE string_utilities,                ONLY: s2a
      42             : #include "../base/base_uses.f90"
      43             : 
      44             :    IMPLICIT NONE
      45             :    PRIVATE
      46             : 
      47             :    LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .TRUE.
      48             :    CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_vib'
      49             : 
      50             :    PUBLIC :: create_vib_section
      51             : CONTAINS
      52             : 
      53             : ! **************************************************************************************************
      54             : !> \brief Creates the exteranal restart section
      55             : !> \param section the section to create
      56             : !> \author tlaino
      57             : ! **************************************************************************************************
      58        8392 :    SUBROUTINE create_vib_section(section)
      59             :       TYPE(section_type), POINTER                        :: section
      60             : 
      61             :       TYPE(keyword_type), POINTER                        :: keyword
      62             :       TYPE(section_type), POINTER                        :: subsection
      63             : 
      64        8392 :       CPASSERT(.NOT. ASSOCIATED(section))
      65             :       CALL section_create( &
      66             :          section, __LOCATION__, name="VIBRATIONAL_ANALYSIS", &
      67             :          description="Section to setup parameters to perform a Normal Modes, vibrational, or phonon analysis. "// &
      68             :          "Vibrations are computed using finite differences, "// &
      69             :          "which implies a very tight (e.g. 1E-8) threshold is needed for EPS_SCF to get accurate low frequencies. "// &
      70             :          "The analysis assumes a stationary state (minimum or TS),"// &
      71             :          " i.e. tight geometry optimization (MAX_FORCE) is needed as well.", &
      72        8392 :          n_keywords=1, n_subsections=0, repeats=.FALSE.)
      73        8392 :       NULLIFY (keyword, subsection)
      74             : 
      75             :       CALL keyword_create(keyword, __LOCATION__, name="DX", &
      76             :                           description="Specify the increment to be used to construct the HESSIAN with "// &
      77             :                           "finite difference method", &
      78        8392 :                           default_r_val=1.0E-2_dp, unit_str="bohr")
      79        8392 :       CALL section_add_keyword(section, keyword)
      80        8392 :       CALL keyword_release(keyword)
      81             : 
      82             :       CALL keyword_create(keyword, __LOCATION__, name="NPROC_REP", &
      83             :                           description="Specify the number of processors to be used per replica "// &
      84             :                           "environment (for parallel runs). "// &
      85             :                           "In case of mode selective calculations more than one replica will start"// &
      86             :                           " a block Davidson algorithm to track more than only one frequency", &
      87        8392 :                           default_i_val=1)
      88        8392 :       CALL section_add_keyword(section, keyword)
      89        8392 :       CALL keyword_release(keyword)
      90             : 
      91             :       CALL keyword_create(keyword, __LOCATION__, name="PROC_DIST_TYPE", &
      92             :                           description="Specify the topology of the mapping of processors into replicas.", &
      93             :                           usage="PROC_DIST_TYPE (INTERLEAVED|BLOCKED)", &
      94             :                           enum_c_vals=s2a("INTERLEAVED", &
      95             :                                           "BLOCKED"), &
      96             :                           enum_desc=s2a("Interleaved distribution", &
      97             :                                         "Blocked distribution"), &
      98             :                           enum_i_vals=(/do_rep_interleaved, do_rep_blocked/), &
      99        8392 :                           default_i_val=do_rep_blocked)
     100        8392 :       CALL section_add_keyword(section, keyword)
     101        8392 :       CALL keyword_release(keyword)
     102             : 
     103             :       CALL keyword_create(keyword, __LOCATION__, name="FULLY_PERIODIC", &
     104             :                           description="Avoids to clean rotations from the Hessian matrix.", &
     105        8392 :                           default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
     106        8392 :       CALL section_add_keyword(section, keyword)
     107        8392 :       CALL keyword_release(keyword)
     108             : 
     109             :       CALL keyword_create(keyword, __LOCATION__, name="INTENSITIES", &
     110             :                           description="Calculation of the IR/Raman-Intensities. "// &
     111             :                           "Calculation of dipoles and/or polarizabilities have to be "// &
     112             :                           "specified explicitly in DFT/PRINT/MOMENTS and/or "// &
     113             :                           "PROPERTIES/LINRES/POLAR", &
     114        8392 :                           default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
     115        8392 :       CALL section_add_keyword(section, keyword)
     116        8392 :       CALL keyword_release(keyword)
     117             : 
     118             :       CALL keyword_create(keyword, __LOCATION__, name="THERMOCHEMISTRY", &
     119             :                           description="Calculation of the thermochemical data. Valid for molecules in the gas phase. ", &
     120        8392 :                           default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
     121        8392 :       CALL section_add_keyword(section, keyword)
     122        8392 :       CALL keyword_release(keyword)
     123             : 
     124             :       CALL keyword_create(keyword, __LOCATION__, name="TC_TEMPERATURE", &
     125             :                           description="Temperature for the calculation of the thermochemical data ", &
     126             :                           usage="tc_temperature 325.0", default_r_val=cp_unit_to_cp2k(value=273.150_dp, unit_str="K"), &
     127        8392 :                           unit_str="K")
     128        8392 :       CALL section_add_keyword(section, keyword)
     129        8392 :       CALL keyword_release(keyword)
     130             : 
     131             :       CALL keyword_create(keyword, __LOCATION__, name="TC_PRESSURE", &
     132             :                           description="Pressure for the calculation of the thermochemical data  ", &
     133        8392 :                           default_r_val=cp_unit_to_cp2k(value=101325.0_dp, unit_str="Pa"), unit_str="Pa")
     134        8392 :       CALL section_add_keyword(section, keyword)
     135        8392 :       CALL keyword_release(keyword)
     136             : 
     137        8392 :       CALL create_mode_selective_section(subsection)
     138        8392 :       CALL section_add_subsection(section, subsection)
     139        8392 :       CALL section_release(subsection)
     140             : 
     141        8392 :       CALL create_print_vib_section(subsection)
     142        8392 :       CALL section_add_subsection(section, subsection)
     143        8392 :       CALL section_release(subsection)
     144        8392 :    END SUBROUTINE create_vib_section
     145             : 
     146             : ! **************************************************************************************************
     147             : !> \brief Create the print section for VIB
     148             : !> \param section the section to create
     149             : !> \author Teodoro Laino [tlaino] - 10.2008
     150             : ! **************************************************************************************************
     151        8392 :    SUBROUTINE create_print_vib_section(section)
     152             :       TYPE(section_type), POINTER                        :: section
     153             : 
     154             :       TYPE(keyword_type), POINTER                        :: keyword
     155             :       TYPE(section_type), POINTER                        :: print_key
     156             : 
     157        8392 :       CPASSERT(.NOT. ASSOCIATED(section))
     158             :       CALL section_create(section, __LOCATION__, name="PRINT", &
     159             :                           description="Section controlling the print information during a vibrational "// &
     160        8392 :                           "analysis.", n_keywords=1, n_subsections=0, repeats=.FALSE.)
     161        8392 :       NULLIFY (keyword, print_key)
     162             : 
     163             :       CALL cp_print_key_section_create(print_key, __LOCATION__, "BANNER", &
     164             :                                        description="Controls the printing of the vibrational analysis banner", &
     165             :                                        print_level=low_print_level, common_iter_levels=1, &
     166        8392 :                                        filename="__STD_OUT__")
     167        8392 :       CALL section_add_subsection(section, print_key)
     168        8392 :       CALL section_release(print_key)
     169             : 
     170             :       CALL cp_print_key_section_create(print_key, __LOCATION__, "PROGRAM_RUN_INFO", &
     171             :                                        description="Controls the printing basic info about the vibrational method", &
     172        8392 :                                        print_level=medium_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
     173        8392 :       CALL section_add_subsection(section, print_key)
     174        8392 :       CALL section_release(print_key)
     175             : 
     176             :       CALL cp_print_key_section_create(print_key, __LOCATION__, "MOLDEN_VIB", &
     177             :                                        description="Controls the printing for visualization in molden format", &
     178        8392 :                                        print_level=low_print_level, add_last=add_last_numeric, filename="VIBRATIONS")
     179        8392 :       CALL section_add_subsection(section, print_key)
     180        8392 :       CALL section_release(print_key)
     181             : 
     182             :       CALL cp_print_key_section_create(print_key, __LOCATION__, "ROTATIONAL_INFO", &
     183             :                                        description="Controls the printing basic info during the cleaning of the "// &
     184             :                                        "rotational degrees of freedom.", &
     185        8392 :                                        print_level=debug_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
     186             :       ! Print_key keywords
     187             :       CALL keyword_create(keyword, __LOCATION__, name="COORDINATES", &
     188             :                           description="Prints atomic coordinates after rotation", &
     189        8392 :                           default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
     190        8392 :       CALL section_add_keyword(print_key, keyword)
     191        8392 :       CALL keyword_release(keyword)
     192        8392 :       CALL section_add_subsection(section, print_key)
     193        8392 :       CALL section_release(print_key)
     194             : 
     195             :       CALL cp_print_key_section_create(print_key, __LOCATION__, "CARTESIAN_EIGS", &
     196             :                                        description="Controls the printing of Cartesian "// &
     197             :                                        "frequencies and eigenvectors of the Hessian used "// &
     198             :                                        "for initializing ensemble for MD calculations. "// &
     199             :                                        "This should always print to a file, and will not "// &
     200             :                                        "effect the same frequencies and eigenvectors printed "// &
     201             :                                        "in the main vibrational analysis output", &
     202             :                                        print_level=low_print_level, &
     203             :                                        add_last=add_last_numeric, &
     204        8392 :                                        filename="VIBRATIONS")
     205             :       CALL keyword_create(keyword, __LOCATION__, name="BACKUP_COPIES", &
     206             :                           description="Specifies the maximum number of backup copies.", &
     207             :                           usage="BACKUP_COPIES {int}", &
     208        8392 :                           default_i_val=1)
     209        8392 :       CALL section_add_keyword(print_key, keyword)
     210        8392 :       CALL keyword_release(keyword)
     211        8392 :       CALL section_add_subsection(section, print_key)
     212        8392 :       CALL section_release(print_key)
     213             : 
     214             :       CALL cp_print_key_section_create(print_key, __LOCATION__, name="NAMD_PRINT", &
     215             :                                        description="Adjust cartesian eigenvalues / vectors to NewtonX format.", &
     216             :                                        print_level=debug_print_level + 1, add_last=add_last_numeric, &
     217        8392 :                                        filename="FullNormalizedCartesian")
     218             :       CALL keyword_create(keyword, __LOCATION__, name="BACKUP_COPIES", &
     219             :                           description="Specifies the maximum number of backup copies.", &
     220             :                           usage="BACKUP_COPIES {int}", &
     221        8392 :                           default_i_val=1)
     222        8392 :       CALL section_add_keyword(print_key, keyword)
     223        8392 :       CALL keyword_release(keyword)
     224        8392 :       CALL section_add_subsection(section, print_key)
     225        8392 :       CALL section_release(print_key)
     226             : 
     227             :       CALL cp_print_key_section_create(print_key, __LOCATION__, "HESSIAN", &
     228             :                                        description="Write the Hessian matrix from a vibrational analysis calculation "// &
     229             :                                        "into a binary file.", &
     230        8392 :                                        print_level=low_print_level, add_last=add_last_numeric, filename="Hessian")
     231        8392 :       CALL section_add_subsection(section, print_key)
     232        8392 :       CALL section_release(print_key)
     233             : 
     234        8392 :    END SUBROUTINE create_print_vib_section
     235             : 
     236             : ! **************************************************************************************************
     237             : !> \brief Create the input section for MODE selective
     238             : !> \param section the section to create
     239             : !> \author fschiff
     240             : ! **************************************************************************************************
     241        8392 :    SUBROUTINE create_mode_selective_section(section)
     242             :       TYPE(section_type), POINTER                        :: section
     243             : 
     244             :       TYPE(keyword_type), POINTER                        :: keyword
     245             :       TYPE(section_type), POINTER                        :: print_key, subsection
     246             : 
     247        8392 :       NULLIFY (keyword, subsection, print_key)
     248        8392 :       CPASSERT(.NOT. ASSOCIATED(section))
     249             :       CALL section_create(section, __LOCATION__, name="MODE_SELECTIVE", &
     250             :                           description="All parameters needed for to run a mode selective vibrational analysis. "// &
     251             :                           "The keywords FREQUENCY, RANGE, and the subsection INVOLVED_ATOMS are mutually exclusive.", &
     252        8392 :                           n_keywords=8, n_subsections=1, repeats=.FALSE.)
     253             : 
     254             :       CALL keyword_create(keyword, __LOCATION__, name="FREQUENCY", &
     255             :                           description="value close to the expected value of the frequency to look for. "// &
     256             :                           "If the block Davidson algorithm is applied, the nrep closest frequencies are tracked. ", &
     257        8392 :                           usage="FREQUENCY {REAL}", default_r_val=-1._dp)
     258        8392 :       CALL section_add_keyword(section, keyword)
     259        8392 :       CALL keyword_release(keyword)
     260             : 
     261             :       CALL keyword_create(keyword, __LOCATION__, name="RANGE", &
     262             :                           description="Track modes in a given range of frequencies. "// &
     263             :                           "No warranty that the set of frequencies is complete.", &
     264             :                           usage="RANGE {REAL} {REAL}", &
     265        8392 :                           n_var=-1, type_of_var=real_t)
     266        8392 :       CALL section_add_keyword(section, keyword)
     267        8392 :       CALL keyword_release(keyword)
     268             : 
     269             :       CALL keyword_create(keyword, __LOCATION__, name="LOWEST_FREQUENCY", &
     270             :                           description="Lowest frequency mode to include when writing output. "// &
     271             :                           "Use a negative value to print imaginary frequencies. "// &
     272             :                           "Useful for visualizing the imaginary frequency along a reaction path coordinate "// &
     273             :                           "Depending on accuracy settings, the output might include spurious low frequency "// &
     274             :                           "imaginary modes which should be visually checked (see MOLDEN_VIB).", &
     275        8392 :                           usage="LOWEST_FREQUENCY <REAL>", default_r_val=0.0_dp)
     276        8392 :       CALL section_add_keyword(section, keyword)
     277        8392 :       CALL keyword_release(keyword)
     278             : 
     279             :       CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
     280             :                           description="Specifies the list of atoms which should be displaced for the Initial guess", &
     281             :                           usage="ATOMS {integer} {integer} .. {integer}", &
     282        8392 :                           n_var=-1, type_of_var=integer_t)
     283        8392 :       CALL section_add_keyword(section, keyword)
     284        8392 :       CALL keyword_release(keyword)
     285             : 
     286             :       CALL keyword_create(keyword, __LOCATION__, name="EPS_MAX_VAL", &
     287             :                           description="Convergence criterion for the davidson algorithm. Specifies the maximal value in the "// &
     288             :                           "residuum vectors ", &
     289        8392 :                           usage="EPS_MAX_VAL {REAL}", default_r_val=5.0E-7_dp)
     290        8392 :       CALL section_add_keyword(section, keyword)
     291        8392 :       CALL keyword_release(keyword)
     292             : 
     293             :       CALL keyword_create( &
     294             :          keyword, __LOCATION__, name="EPS_NORM", &
     295             :          description="Convergence criterion for the davidson algorithm. Specifies the maximal value of the norm "// &
     296             :          "of the residuum vectors ", &
     297        8392 :          usage="EPS_NORM {REAL}", default_r_val=2.0E-6_dp)
     298        8392 :       CALL section_add_keyword(section, keyword)
     299        8392 :       CALL keyword_release(keyword)
     300             : 
     301             :       CALL keyword_create( &
     302             :          keyword, __LOCATION__, name="INITIAL_GUESS", &
     303             :          description="The type of initial guess for the normal modes", &
     304             :          usage="INITIAL_GUESS BFGS_HESS", &
     305             :          default_i_val=ms_guess_atomic, &
     306             :          enum_c_vals=s2a("BFGS_HESS", "ATOMIC", "RESTART", "RESTART_VEC", "MOLDEN_RESTART"), &
     307             :          enum_desc=s2a("get the first displacement vector out of the BFGS approximate Hessian", &
     308             :                        "use random displacements for a set of atoms specified", &
     309             :                        "use data from MS_RESTART as initial guess", &
     310             :                        "use a vector from MS_RESTART, useful if you want to increase accurcy by changing functionals or basis", &
     311             :                        "use the .mol file of a former run, to restart a vector"// &
     312             :                        " (similar to Restart_vec, but a different file FORMAT is used)"), &
     313        8392 :          enum_i_vals=(/ms_guess_bfgs, ms_guess_atomic, ms_guess_restart, ms_guess_restart_vec, ms_guess_molden/))
     314        8392 :       CALL section_add_keyword(section, keyword)
     315        8392 :       CALL keyword_release(keyword)
     316             : 
     317             :       CALL keyword_create(keyword, __LOCATION__, name="RESTART_FILE_NAME", &
     318             :                           description="Specifies the name of the file used to create the restarted vectors", &
     319             :                           usage="RESTART_FILE_NAME {filename}", &
     320        8392 :                           default_lc_val="")
     321        8392 :       CALL section_add_keyword(section, keyword)
     322        8392 :       CALL keyword_release(keyword)
     323             : 
     324        8392 :       CALL create_involved_atoms_section(subsection)
     325        8392 :       CALL section_add_subsection(section, subsection)
     326        8392 :       CALL section_release(subsection)
     327             : 
     328             :       CALL section_create(subsection, __LOCATION__, name="PRINT", &
     329             :                           description="Controls the printing mode selective vibrational analysis", &
     330        8392 :                           n_keywords=0, n_subsections=1, repeats=.TRUE.)
     331             : 
     332             :       CALL cp_print_key_section_create(print_key, __LOCATION__, "MS_RESTART", &
     333             :                                        description="Controls the printing of the Mode Selective Restart file.", &
     334             :                                        print_level=silent_print_level, common_iter_levels=1, &
     335        8392 :                                        add_last=add_last_numeric, filename="")
     336        8392 :       CALL section_add_subsection(subsection, print_key)
     337        8392 :       CALL section_release(print_key)
     338             : 
     339        8392 :       CALL section_add_subsection(section, subsection)
     340        8392 :       CALL section_release(subsection)
     341             : 
     342        8392 :    END SUBROUTINE create_mode_selective_section
     343             : 
     344             : ! **************************************************************************************************
     345             : !> \brief Create the input section for Ivolved_atoms keyword in mode selective
     346             : !> \param section the section to create
     347             : !> \author fschiff
     348             : ! **************************************************************************************************
     349        8392 :    SUBROUTINE create_involved_atoms_section(section)
     350             :       TYPE(section_type), POINTER                        :: section
     351             : 
     352             :       TYPE(keyword_type), POINTER                        :: keyword
     353             : 
     354        8392 :       NULLIFY (keyword)
     355        8392 :       CPASSERT(.NOT. ASSOCIATED(section))
     356             :       CALL section_create( &
     357             :          section, __LOCATION__, name="INVOLVED_ATOMS", &
     358             :          description="All parameters needed for the tracking of modes dominated by the motion of selected atoms. "// &
     359             :          "Warning, if many atoms are involved, only low frequency modes are detected, "// &
     360             :          "since they are more delocalized and match the tracked eigenvector.", &
     361        8392 :          n_keywords=2, n_subsections=0, repeats=.FALSE.)
     362             : 
     363             :       CALL keyword_create( &
     364             :          keyword, __LOCATION__, name="RANGE", &
     365             :          description=" Specifies the range of wavenumbers in which the modes related to the ATOMS have to be tracked."// &
     366             :          " If not specified frequencies >400cm-1 will be used to avoid tracking of translational or rotational modes", &
     367             :          usage="RANGE {REAL} {REAL}", &
     368        8392 :          n_var=-1, type_of_var=real_t)
     369        8392 :       CALL section_add_keyword(section, keyword)
     370        8392 :       CALL keyword_release(keyword)
     371             : 
     372             :       CALL keyword_create( &
     373             :          keyword, __LOCATION__, name="INVOLVED_ATOMS", &
     374             :          description="Specifies the list of atoms on which the tracked eigenvector should have the highest value "// &
     375             :          "similar to looking for the vibration of a set of atoms", &
     376             :          usage="INVOLVED_ATOMS {integer} {integer} .. {integer}", &
     377        8392 :          n_var=-1, type_of_var=integer_t)
     378        8392 :       CALL section_add_keyword(section, keyword)
     379        8392 :       CALL keyword_release(keyword)
     380             : 
     381        8392 :    END SUBROUTINE create_involved_atoms_section
     382             : 
     383             : END MODULE input_cp2k_vib

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